- Implement parallelised processing
- Warn once when exchange is missing from model
- Draft output
- optimisiation value
- command/code to collate all optimisation codes into single table
- pass/fail, optimisation value, media
- Investigate lack of translations in CDS featuers for reannotated assemblies
- Clean up file i/o in annotation
- specifically matching ORFs
- Clean up code in general
- Handle spontaneous genes better
- Check required programs are in PATH and have correct versions
- Getting 1182 orthologs on K_quasi_quasi_01A030T, tut notes have 1186
- 1185 after unannotated gene search (tut detected no annotated genes)
- resolve differences
- Test BLASTn alignment sequence extraction
- ensure bounds are correct, no off-by-one errors